Reviewed, UniProtKB/Swiss-Prot P31896 (COOS_RHORU)

Names and origin

Protein names

Recommended name:
    Carbon monoxide dehydrogenase
      Short name=CODH
    EC=1.2.99.2

Gene names

Name:

cooS

Organism

Rhodospirillum rubrum

Taxonomic identifier

1085 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodospirillales › Rhodospirillaceae › Rhodospirillum

Protein attributes

Sequence length	639 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Allows growth in a CO-dependent manner in the dark. CODH oxidizes carbon monoxide coupled, via cooF, to the reduction of a hydrogen cation by a hydrogenase (possibly cooH).
Catalytic activity	CO + H2O + A = CO2 + AH2.
Cofactor	Binds 3 4Fe-4S clusters per homodimer. Binds 2 nickel-iron-sulfur clusters per homodimer.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm. Cell inner membrane; Peripheral membrane protein; Cytoplasmic side. Note: Loosely attached to the inner membrane, probably via cooF By similarity.
Induction	By carbon monoxide; under anaerobic conditions.
Domain	Cluster B is an all-cysteinyl-liganded 4Fe4S cluster; cluster C is a mixed Ni-Fe-S cluster which appears to be the active site of CO oxidation. Cluster D is also an all-cysteinyl-liganded 4Fe4S cluster that bridges the two subunits of the CODH dimer.
Miscellaneous	Methyl viologen can act as acceptor. Inactivated by O2.
Sequence similarities	Belongs to the Ni-containing carbon monoxide dehydrogenase family.

Ontologies

Keywords
Cellular component	Cell inner membrane Cell membrane Cytoplasm Membrane
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding Nickel
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	generation of precursor metabolites and energy Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW carbon-monoxide dehydrogenase (acceptor) activity Inferred from electronic annotation. Source: EC electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 639

639

Carbon monoxide dehydrogenase

PRO_0000157139

Sites

Metal binding

41

1

Iron-sulfur 1 (4Fe-4S); shared with dimeric partner

Metal binding

49

1

Iron-sulfur 1 (4Fe-4S); shared with dimeric partner

Metal binding

50

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

53

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

58

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

72

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

265

1

Nickel-iron-sulfur (Ni-4Fe-4S); via tele nitrogen

Metal binding

300

1

Nickel-iron-sulfur (Ni-4Fe-4S)

Metal binding

338

1

Nickel-iron-sulfur (Ni-4Fe-4S)

Metal binding

451

1

Nickel-iron-sulfur (Ni-4Fe-4S)

Metal binding

481

1

Nickel-iron-sulfur (Ni-4Fe-4S)

Metal binding

531

1

Nickel-iron-sulfur (Ni-4Fe-4S)

Experimental info

Mutagenesis

265

1

H → V: Great decrease in activity; diminishes incorporation of nickel. Displays hydroxylamine reductase activity. Ref.3

Mutagenesis

531

1

C → A: Displays hydrogenase activity. Ref.4

Secondary structure

1

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639

Helix Strand Turn

Details...

Helix

30 – 37

8

Helix

42 – 46

5

Beta strand

62 – 66

5

Helix

76 – 109

34

Turn

110 – 112

3

Helix

122 – 131

10

Turn

137 – 139

3

Helix

141 – 154

14

Turn

155 – 157

3

Helix

166 – 171

6

Helix

174 – 183

10

Helix

190 – 200

11

Helix

209 – 238

30

Beta strand

244 – 250

7

Beta strand

257 – 265

9

Helix

267 – 279

13

Turn

280 – 282

3

Helix

283 – 286

4

Beta strand

292 – 298

7

Helix

299 – 308

10

Beta strand

313 – 315

3

Turn

318 – 321

4

Helix

322 – 325

4

Beta strand

331 – 334

4

Beta strand

336 – 338

3

Helix

343 – 348

6

Beta strand

353 – 356

4

Beta strand

366 – 368

3

Helix

373 – 375

3

Helix

376 – 391

16

Beta strand

406 – 410

5

Helix

414 – 422

9

Helix

430 – 439

10

Beta strand

440 – 442

3

Beta strand

444 – 448

5

Helix

460 – 471

12

Beta strand

474 – 479

6

Helix

480 – 489

10

Helix

494 – 500

7

Helix

503 – 515

13

Beta strand

518 – 520

3

Beta strand

524 – 531

8

Helix

534 – 547

14

Turn

552 – 554

3

Beta strand

555 – 561

7

Helix

567 – 579

13

Beta strand

582 – 587

6

Turn

590 – 593

4

Helix

595 – 602

8

Helix

604 – 608

5

Beta strand

612 – 615

4

Helix

619 – 635

17

Sequences

	Sequence		Length	Mass (Da)
	P31896-1 [UniParc]. Last modified July 1, 1993. Version 1. Checksum: DCADD7C13D8D85B8	FASTA	639	66,854
	10 20 30 40 50 60 MTHHDCAHCS SDACATEMLN LAEANSIETA WHRYEKQQPQ CGFGSAGLCC RICLKGPCRI 70 80 90 100 110 120 DPFGEGPKYG VCGADRDTIV ARHLVRMIAA GTAAHSEHGR HIALAMQHIS QGELHDYSIR 130 140 150 160 170 180 DEAKLYAIAK TLGVATEGRG LLAIVGDLAA ITLGDFQNQD YDKPCAWLAA SLTPRRVKRL 190 200 210 220 230 240 GDLGLLPHNI DASVAQTMSR THVGCDADPT NLILGGLRVA MADLDGSMLA TELSDALFGT 250 260 270 280 290 300 PQPVVSAANL GVMKRGAVNI AVNGHNPMLS DIICDVAADL RDEAIAAGAA EGINIIGICC 310 320 330 340 350 360 TGHEVMMRHG VPLATNYLSQ ELPILTGALE AMVVDVQCIM PSLPRIAECF HTQIITTDKH 370 380 390 400 410 420 NKISGATHVP FDEHKAVETA KTIIRMAIAA FGRRDPNRVA IPAFKQKSIV GFSAEAVVAA 430 440 450 460 470 480 LAKVNADDPL KPLVDNVVNG NIQGIVLFVG CNTTKVQQDS AYVDLAKSLA KRNVLVLATG 490 500 510 520 530 540 CAAGAFAKAG LMTSEATTQY AGEGLKGVLS AIGTAAGLGG PLPLVMHMGS CVDNSRAVAL 550 560 570 580 590 600 ATALANKLGV DLSDLPLVAS APECMSEKAL AIGSWAVTIG LPTHVGSVPP VIGSQIVTKL 610 620 630 VTETAKDLVG GYFIVDTDPK SAGDKLYAAI QERRAGLGL

References

[1]	"Genetic and physiological characterization of the Rhodospirillum rubrum carbon monoxide dehydrogenase system." Kerby R.L., Hong S.S., Ensign S.A., Coppoc L.J., Ludden P.W., Roberts G.P. J. Bacteriol. 174:5284-5294(1992) [PubMed: 1644755] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: UR1.
[2]	"Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme." Fox J.D., Kerby R.L., Roberts G.P., Ludden P.W. J. Bacteriol. 178:1515-1524(1996) [PubMed: 8626276] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: UR1.
[3]	"Substitution of valine for histidine 265 in carbon monoxide dehydrogenase from Rhodospirillum rubrum affects activity and spectroscopic states." Spangler N.J., Meyers M.R., Gierke K.L., Kerby R.L., Roberts G.P., Ludden P.W. J. Biol. Chem. 273:4059-4064(1998) [PubMed: 9461598] [Abstract] Cited for: MUTAGENESIS OF HIS-265.
[4]	"Converting the NiFeS carbon monoxide dehydrogenase to a hydrogenase and a hydroxylamine reductase." Heo J., Wolfe M.T., Staples C.R., Ludden P.W. J. Bacteriol. 184:5894-5897(2002) [PubMed: 12374822] [Abstract] Cited for: MUTAGENESIS OF CYS-531.
[5]	"CO dehydrogenase." Ferry J.G. Annu. Rev. Microbiol. 49:305-333(1995) [PubMed: 8561463] [Abstract] Cited for: REVIEW.
[6]	"Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase." Drennan C.L., Heo J., Sintchak M.D., Schreiter E., Ludden P.W. Proc. Natl. Acad. Sci. U.S.A. 98:11973-11978(2001) [PubMed: 11593006] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).

Cross-references

Sequence databases

EMBLGenBankDDBJ

U65510 Genomic DNA. Translation: AAC45123.1.

PIR

C42957.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JQK	X-ray	2.80	A/B/C/D/E/F	1-639	[»]

DisProt

DP00239.

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.2.99.2. 1671.

Family and domain databases

InterPro

IPR016101. CO_DH_a-bundle.
IPR010047. CO_DH_cat.
IPR004137. Prismane.
IPR016099. Prismane-like_a/b-sand.
[Graphical view]

Gene3D

G3DSA:1.20.1270.30. CO_DH_a-bundle. 1 hit.
G3DSA:3.40.50.2030. Prismane-like_a/b-sand. 1 hit.

Pfam

PF03063. Prismane. 1 hit.
[Graphical view]

PIRSF

PIRSF005023. CODH. 1 hit.

TIGRFAMs

TIGR01702. CO_DH_cata. 1 hit.

ProtoNet

Search...

Entry information

Entry name

COOS_RHORU

Accession

Primary (citable) accession number: P31896

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	June 16, 2009
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)